Do you get the "No fish to catch" announcement, or do they just not catch anything? You won't get shells by embarking with lobsters/turtles anymore -- you have to get shells via "Prepare raw fish" at a Fishery.

I did a second fortress, again with both ponds and river, and the results are the same : Nothing everywhere. My fisherdwarf goes to fish, stays still a moment, then declares that there isn't any fish in this pond/river. He then goes to the next area to start all over again.